Dataset Information

EGAS00001000262-sc-20140722b - samples

ABSTRACT: Whole Genome Sequencing Illumina HiSeq data from 20 men with prostate cancer. 20 samples were taken from primary tissue obtained at prostatectomy (target sequencing depth 50X) with matched blood control (target sequencing depth 30X). These were submitted for use in the ICGC Pan-Cancer Analysis of Whole Genomes project. Same raw data submitted in EGAD00001001116. As of September 2020, some of the studies using these data include: Wedge et al, Nature Genetics 2018 (PMID: 29662167) Pan-Cancer Analysis of Whole Genomes, Nature 2020 (PMID: 32025007)

PROVIDER: EGAD00001000892 | EGA |

REPOSITORIES: EGA

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Publications

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets.

Wedge David C DC Gundem Gunes G Mitchell Thomas T Woodcock Dan J DJ Martincorena Inigo I Ghori Mohammed M Zamora Jorge J Butler Adam A Whitaker Hayley H Kote-Jarai Zsofia Z Alexandrov Ludmil B LB Van Loo Peter P Massie Charlie E CE Dentro Stefan S Warren Anne Y AY Verrill Clare C Berney Dan M DM Dennis Nening N Merson Sue S Hawkins Steve S Howat William W Lu Yong-Jie YJ Lambert Adam A Kay Jonathan J Kremeyer Barbara B Karaszi Katalin K Luxton Hayley H Camacho Niedzica N Marsden Luke L Edwards Sandra S Matthews Lucy L Bo Valeria V Leongamornlert Daniel D McLaren Stuart S Ng Anthony A Yu Yongwei Y Zhang Hongwei H Dadaev Tokhir T Thomas Sarah S Easton Douglas F DF Ahmed Mahbubl M Bancroft Elizabeth E Fisher Cyril C Livni Naomi N Nicol David D Tavaré Simon S Gill Pelvender P Greenman Christopher C Khoo Vincent V Van As Nicholas N Kumar Pardeep P Ogden Christopher C Cahill Declan D Thompson Alan A Mayer Erik E Rowe Edward E Dudderidge Tim T Gnanapragasam Vincent V Shah Nimish C NC Raine Keiran K Jones David D Menzies Andrew A Stebbings Lucy L Teague Jon J Hazell Steven S Corbishley Cathy C de Bono Johann J Attard Gerhardt G Isaacs William W Visakorpi Tapio T Fraser Michael M Boutros Paul C PC Bristow Robert G RG Workman Paul P Sander Chris C Hamdy Freddie C FC Futreal Andrew A McDermott Ultan U Al-Lazikani Bissan B Lynch Andrew G AG Bova G Steven GS Foster Christopher S CS Brewer Daniel S DS Neal David E DE Cooper Colin S CS Eeles Rosalind A RA

Nature genetics 20180416 5

Prostate cancer represents a substantial clinical challenge because it is difficult to predict outcome and advanced disease is often fatal. We sequenced the whole genomes of 112 primary and metastatic prostate cancer samples. From joint analysis of these cancers with those from previous studies (930 cancers in total), we found evidence for 22 previously unidentified putative driver genes harboring coding mutations, as well as evidence for NEAT1 and FOXA1 acting as drivers through noncoding mutat ...[more]

PMID: 29662167

Publication: 1/2

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Project description:Full title: Probing the pan genome of a foodborne bacterial pathogen Listeria monocytogenes: Implications for its niche adaptation, pathogenesis, and evolution Listeria monocytogenes is a foodborne bacterial pathogen well known for adaptability to diverse environmental and host niches, and a high fatality rate among infected, immuno-compromised individuals. Three genetic lineages have been identified within this species. Strains of genetic lineages I and II account for more than ninety percent of foodborne disease outbreaks worldwide, whereas strains from genetic lineage III are rarely implicated in human infectious for unknown, yet intriguing, reasons. Here we have probed the genomic diversity of 26 L. monocytogenes strains using both whole-genome sequences and a novel 385,000 probe pan-genome microarray, fully tiling the genomes of 20 representative strains. Using these methods to identify genes highly conserved in lineages I and II but rare in lineage III, we have identified 86 genes and 8 small RNAs that play roles in bacterial stress resistance, pathogenicity, and niche, potentially explaining the predominance of L. monocytogenes lineages I and II in foodborne disease outbreaks. Extending gene content analysis to all lineages revealed a L. monocytogenes core genome of approximately 2,350 genes (80% of each individual genome) and a pan-genomic reservoir of >4,000 unique genes. Combined gene content data from both sequences and arrays was used to reconstruct an informative phylogeny for the L. monocytogenes species that confirms three distinct lineages and describes the relationship of 9 new lineage III genomes. Comparative analysis of 18 fully sequenced L. monocytogenes lineage I and II genomes shows a high level of genomic conservation and synteny, indicative of a closed pan-genome, with moderate domain shuffling and sequence drift associated with bacteriophages is present in all lineages. In contrast with lineages I and II, notable genomic diversity and characteristics of an open pan-genome were observed in the lineage III genomes, including many strain-specific genes and a more complex conservation pattern. This indicates that the L. monocytogenes pan-genome has not yet been fully sampled by genome sequencing, and additional sequencing of lineage III genomes is necessary to survey the full diversity of this intriguing species and reveal its mechanisms for adaptability and virulence. This is a Listeria monocytogenes pan-genome tilling array designed using PanArray algorithm. 9 experimental strains (F2-569, M1-002, F2-208, J2-071, J1-208, W1-111, W1-110, F2-524, F2-501) vs reference (EGD-e) strain.

Dataset Information

EGAS00001000262-sc-20140722b - samples

Publications

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets.

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